I am posting here, hoping for ideas and feedback on how we can use the computer to
1) improve biomedical research, especially in cancer, and at the same time
2) reduce the use of laboratory animals.

My professional background is that I recently started as a bioinformatic engineer in a cancer research institute.

Biomedical science seems to be seriously hampered by the use of animal models, as Khalil writes in a recent article in Current view on Oncology:
"Many of the cell lines and animal models used to study cancer mechanisms and test possible therapeutics are not predictive of what will happen in actual in vivo human tumors. The discrepancy between in vitro and the in vivo human has significantly affected the ability of researchers to devise successful cancer therapeutics. “(1)

An example of the problem with the animal model is shown in the case of DNA (plasmid) vaccination. Although successul in animal models in humans it didnot work that well:
* However It soon became evident that DNA vaccines while robust in small animal models were less immungenic in nonhuman primates and humans. (6). and
* Unfortunately, this (DNA plasmid, ed) technology has not proven to be reliable in humans. (2, p. s7)

Replacing animal models for computermodels based on human (f.e. microarray) data, would improve science and at the same time reduce the use of laboratory animals. Besides the effort in building such models, it also seem to require a paradigma shift in biomedical science. Traditional, biomedical (molecular) science is using a reductionistic approach, Reseach is focused on the effects of knocking down or knocking out of a single gene. A more holistic, system approach is needed. The approach advocated by Khalil is to infer (“reverse engineering”) the gene regulatory mechanisms looking at microarray data, using mathematics and statistics. The “inference engine” should however also take in account what is already known in the form of existing computermodels.

What do you think are the prospects and/or requirements for the use of computer models in stead of animal models in biomedical science?

This is a very interesting idea. But for it to be accomplished and then taken seriously (there will be, as always, skeptics) it must pass a serious number of years. It has a high potential, but you can't model that which you can't understand. And I think the interactions in the body are not fully understood yet. This is the main obstacle.